We were unable to reproduce the reported issue. When we ran the project, the autocomplete multi column with multi select rendered properly. Please ensure that you have referred dependent scripts and CSS files in your application. For you reference, we have prepared a simple Autocomplete MVC application with multi column with multi select enabled. You can get that sample from:
If the problem persists still after using the above, please modify the provided sample based on your application along with the replication procedure to showcase the issue. Or, you can share the code sample of how you had created the Autocomplete with multi column in multi select and share the console errors, if any. This would help us to provide an appropriate solution at the earliest.
Regards, Prasanth P.